Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1709 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg1003464531 sf1003463508 10 3464531 1.20E-134 4.37E-78
vg1003436213 sf1003435190 10 3436213 1.75E-133 1.93E-79
vg1003446306 sf1003445283 10 3446306 2.28E-123 2.03E-75
vg0710493875 sf0710492881 7 10493875 5.39E-35 1.22E-09
vg0717726119 sf0717725126 7 17726119 2.19E-28 7.93E-09
vg0909395154 sf0909394153 9 9395154 3.35E-27 4.61E-09
vg0909393050 sf0909392049 9 9393050 1.66E-26 2.96E-11
vg1209942861 sf1209940271 12 9942861 6.37E-26 1.13E-07
vg0717726887 sf0717725894 7 17726887 7.20E-26 9.60E-11
vg0422509978 sf0422324865 4 22509978 4.45E-23 1.81E-10
vg1209942785 sf1209940195 12 9942785 6.12E-22 3.48E-08
vg0403728354 sf0403723960 4 3728354 6.69E-22 3.22E-09
vg1003047386 sf1003046363 10 3047386 4.89E-20 1.70E-13
vg0909083757 sf0909082756 9 9083757 2.71E-18 1.01E-07
vg1003128682 sf1003127659 10 3128682 3.52E-17 3.89E-16
vg1003688387 sf1003687364 10 3688387 7.24E-17 9.22E-10
vg1003107608 sf1003106585 10 3107608 2.72E-15 1.82E-08
vg1002297086 sf1002296063 10 2297086 6.46E-15 2.95E-07
vg0707298023 sf0707297028 7 7298023 1.45E-13 6.73E-07
vg1003509410 sf1003508387 10 3509410 1.61E-11 1.89E-07
vg0623386254 sf0623385257 6 23386254 1.54E-10 3.60E-10
vg1003378620 sf1003377597 10 3378620 9.43E-10 9.40E-07
vg1003083837 sf1003082814 10 3083837 2.08E-09 9.08E-08
vg0216673470 sf0216667600 2 16673470 9.18E-09 6.63E-07
vg1003373930 sf1003372907 10 3373930 NA 4.05E-10